Nikon D5000 has a
12.0MP APS-C (23.6 x 15.8 mm ) sized CMOS sensor and features Expeed processor. On the other hand, Sigma DP3 Merrill has a
15.0MP APS-C (24 x 16 mm ) sized CMOS (Foveon X3) sensor and features Dual TRUE II engine processor.
Below you can see the D5000 and DP3 Merrill sensor size comparison.
Sensor Size and Resolution Comparison image of Nikon D5000 and Sigma DP3 Merrill Cameras
Nikon D5000 and Sigma DP3 Merrill have almost the same sensor size, so neither of them has any significant advantage over the other in terms of providing control over depth of field when used with the same focal length and aperture.
Sensor size sets the circle of confusion, so it drives how much depth of field each
of these bodies gives you at a given aperture. You can calculate it exactly for the
Nikon D5000
or the
Sigma DP3 Merrill ,
including hyperfocal distance.